Dnarust

I'm still thinking about the name of the lib

A personal project which consists in a basic library for genomics and bioinformatics

Features

• 1. DNA
• 2. Proteins
• 3. FASTA
• 4. File CODEC

See To-do list for current and futures features.

1. DNA

use biorust::dnadir::dna;

fn main() {
    let seq = dna::Sequence::new("ACGTATAC");
    
    println!("Seq: {}", seq);
    println!("Lenght: {}", seq.lenght());
    println!("Complement: {}", seq.complement());
    println!("Reverse complement: {}", seq.reverse_complement());
    println!("Rna: {}", seq.to_rna());
    println!("Reverse Rna: {}", seq.to_reverse_rna());
    println!("GC %: {}", seq.gc_content());
    println!("Translation: {}", seq.translate_as_string());
    println!("{:?}", seq.translate_as_vector());
    println!("{}", seq.translate_as_string3());
}

Output

Seq: ACGTATAC
Lenght: 8
Complement: TGCATATG
Reverse complement: GTATACGT
Rna: ACGUAUAC
Reverse Rna: CAUAUGCA
GC %: 37.5
Translation: TY
[Thr, Tyr]
Thr-Tyr

2. Proteins

use biorust::proteindir::proteins;

fn main (){

    let protein = proteins::Protein::new("ACDEFGHIKLMNPQRSTVWY");

    println!("{}", protein.lenght());
    println!("{:?}", protein.from_string_to_vector());
    println!("{}", protein.protein_weight());
}

Output

20
[Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr]
2395.755

3. FASTA

FASTA READER

use biorust::io::fasta;

fn main() -> std::io::Result<()> {

    let record1 = fasta::read_records("PATH TO FASTA FILE")?;
    let record2 = fasta::read_records("PATH TO FASTA FILE")?;
    let records = fasta::read_records("PATH TO FASTA FILE")?;

    for record in &record2 {
        println!("ID: {}", record.id);

        if let Some(desc) = &record.description {
            println!("Description: {}", desc);
        }
        println!("{}", record.sequence);
    }
    Ok(())
}

FASTA WRITER

use biorust::dnadir::dna::Sequence;
use biorust::io::fasta;

fn main() -> std::io::Result<()> {
    let seq = Sequence::new("ATGGCCTAGCGATAA");
    let seq2 = Sequence::new("GGATGCACGAGCA");

    let record1 = fasta::FastaRecord::new("ID_1".to_string(), seq.clone());
    let record2 = fasta::FastaRecord::new_wd("ID_2".to_string(), "Desc_2".to_string(), seq2.clone());

    fasta::write_record("ouput1.fasta", &record1)?;
    fasta::write_record("ouput2.fasta", &record2)?;
    fasta::write_records("ouput3.fasta", &[record1, record2],
    )?;

    Ok(())
}

4. File CODEC

Encoder: Takes bytes → extracts bit pairs → maps to nucleotides

Decoder: Takes nucleotides → maps to bit pairs → reconstructs bytes

For more information See This

use biorust::io::files;

fn main()-> std::io::Result<()> {

    let input_encoder = "assets/images.jpg";
    let filename_encoder = "assets/prueba.dna";
    let _ = files::encoder(input_encoder, filename_encoder);

    let input_decoder = "assets/prueba.dna";
    let filename_decoder = "assets/recovered.jpg";
    let _ = files::decoder(input_decoder, filename_decoder);

    Ok(())
}

To do list

DNA

• The length of a DNA chain
• Convert DNA squence to its complement
• Convert DNA squence to its reverse complement
• Convert DNA to mRNA
• Calculate GC content
• Translate DNA to polypeptide chain with full amino acid names (e.g., Ala, Arg, Asn)
• Translate DNA to polypeptide chain with single-letter amino acid codes (e.g., A, R, N)
• Convert between single-letter and three-letter amino acid codes

Proteins

• Calculate molecular weight of the protein
• Isoelectric point (pI)
• Find synonymous codons for each amino acid
• Generate silent mutations (synonymous codon substitutions)

Primers designing

• Optimal melting temperature (Tm)
• The Gibbs free energy change (ΔG)
• Avoid long repeats
• 40 < GC% < 60

FASTA

• Reading FASTA files
• Writing FASTA files

Documentation

See Documentation